Journal ArticleDOI
Peptide Folding: When Simulation Meets Experiment
Xavier Daura,Karl Gademann,Bernhard Jaun,Dieter Seebach,Wilfred F. van Gunsteren,Alan E. Mark +5 more
TLDR
Despite the small differences in sequence between the two peptides studied, the simulations correctly predict a left-handed 31-helical fold for the beta-heptapeptide and a right-handed helical Fold for thebeta-hexapeptides.Abstract:
Accurate reproduction of the mechanism of peptide folding in solution and conformational preferences as a function of amino acid sequence is possible with atomic level dynamics simulations. For example, the simulations correctly predict a left-handed 31-helical fold for the β-heptapeptide 1 (the molecular model is shown in the picture) and a right-handed helical fold for the β-hexapeptide 2, as was confirmed by NMR spectroscopy.read more
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TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
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